Description Usage Arguments Value Examples
Calculate the pearson's correlation between microRNA and feature (gene/protein) matrices. The function calls the R base cor function. More importantly the function prepare the input matrices before the call. First, if matches the col.names/bcr. Second, remove duplicated entries. Finally, it removes the microRNAs and features with expression values less than one. In addation, The function returns a tidy data.frame rather than the raw matrix output of cor.
1 |
mi |
A tidy matrix of microRNA expression data. |
m |
A tidy matrix of gene or protein expression data. |
cohort |
A charachter string of the TCGA ID. |
tidy |
A logical |
A tidy data.frame of four columns; miRBase ID, feature id, correlation and TCGA study name.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # load required libraries
library(RTCGA.rnaseq)
library(RTCGA.miRNASeq)
library(RTCGA.RPPA)
# calculate correlation for genes
ACC.mi <- mirna_tidy(ACC.miRNASeq)
ACC.m <- mrna_tidy(ACC.rnaseq)
corr <- cor_make(ACC.mi, ACC.m, 'ACC')
# calculate correlation for proteins
ACC.mi <- mirna_tidy(ACC.miRNASeq)
ACC.r <- rppa_tidy(ACC.RPPA)
corr <- cor_make(ACC.mi, ACC.r, 'ACC')
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